Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015440.1 Corchorus capsularis cultivar CVL-1 contig15461, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 122389
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2346 original size:49 final size:49
Alignment explanation
Indices: 2277--2639 Score: 532
Period size: 49 Copynumber: 7.4 Consensus size: 49
2267 AATTTTCATC
* *
2277 TTTACTTG-TATCTCCCAAAACACCCTTCCCAGACGGAAGCCATTTATT
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
* * *
2325 TTTACTTCCTATTTCCCAAAACGCCCTTCCCAGACGGAAGTCATTCATT
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
*
2374 TTTGCTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
* * * *
2423 TTTACTTGCTATTTCCCAAAGCGCCCTACCCAGACGGAAGCCATTCATC
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
*
2472 TTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATT
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
*
2521 TTTGCTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
* * **
2570 TTTGCTTGTTATTTCCCAAAACGCCCTTCCC-GAACGGAAGGTATTTATT
1 TTTACTTGCTATTTCCCAAAACGCCCTTCCCAG-ACGGAAGCCATTTATT
* * *
2619 CTTACCTGCCATTTCCCAAAA
1 TTTACTTGCTATTTCCCAAAA
2640 TGCCTTTTCC
Statistics
Matches: 286, Mismatches: 27, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
48 8 0.03
49 278 0.97
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (49 bp):
TTTACTTGCTATTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATT
Found at i:3495 original size:31 final size:34
Alignment explanation
Indices: 3460--3522 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
3450 TGACTCCTGG
3460 ATTAAGCC-ATT-T-ATTTACTTAATTACACTAA
1 ATTAAGCCAATTATGATTTACTTAATTACACTAA
3491 ATTAAGCCAATTACTGATTTACTTAATTACAC
1 ATTAAGCCAATTA-TGATTTACTTAATTACAC
3523 CGAAATAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 8 0.29
32 3 0.11
34 1 0.04
35 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (34 bp):
ATTAAGCCAATTATGATTTACTTAATTACACTAA
Found at i:3539 original size:35 final size:35
Alignment explanation
Indices: 3472--3553 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
3462 TAAGCCATTT
* **
3472 ATTTACTTAATTACACTAAATTAAGCCAATTACTG
1 ATTTACTTAATTACACGAAATTAAGCCAATTACCA
***
3507 ATTTACTTAATTACACCGAAA-TAAGTTGATTACCA
1 ATTTACTTAATTACA-CGAAATTAAGCCAATTACCA
*
3542 AATTACTTAATT
1 ATTTACTTAATT
3554 TAATTACAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (35 bp):
ATTTACTTAATTACACGAAATTAAGCCAATTACCA
Found at i:3545 original size:27 final size:27
Alignment explanation
Indices: 3515--3595 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
3505 TGATTTACTT
*
3515 AATTACACCGAAATAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
* *
3542 AATT--A-C---TTAATTTAATTA-CA
1 AATTACACCGAATTAAGTTGATTACCA
3562 AATTTACACCGAATTAAGTTGATTACCA
1 AA-TTACACCGAATTAAGTTGATTACCA
3590 AATTAC
1 AATTAC
3596 TTAATTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
20 4 0.10
21 11 0.27
23 1 0.02
24 2 0.05
25 1 0.02
27 18 0.44
28 4 0.10
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.33
Consensus pattern (27 bp):
AATTACACCGAATTAAGTTGATTACCA
Found at i:3571 original size:48 final size:48
Alignment explanation
Indices: 3517--3608 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
3507 ATTTACTTAA
3517 TTACACCGAAATAAGTTGATTACCAAATTACTTAATTTAATTACAAAT
1 TTACACCGAAATAAGTTGATTACCAAATTACTTAATTTAATTACAAAT
*
3565 TTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTAC
1 TTACACCGAAATAAGTTGATTACCAAATTACTTAATTTAATTAC
3609 CGCTTTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (48 bp):
TTACACCGAAATAAGTTGATTACCAAATTACTTAATTTAATTACAAAT
Found at i:3594 original size:35 final size:35
Alignment explanation
Indices: 3565--3954 Score: 342
Period size: 35 Copynumber: 10.7 Consensus size: 35
3555 AATTACAAAT
3565 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
* ** *
3600 TTTAATTACCGCTTTAA--T--TT-CCAATTTACTTAA
1 -TT-A-CACCGAATTAAGTTGATTACCAAATTACTTAA
*
3633 TTGCACCGAATTAAGTTGATTACCAAATTACTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
* * * *
3668 TTTAATTACCGATTTAATTAATTTAATTTCC-AATATACTTAA
1 -TT-A-CACCG----AATTAAGTTGATTACCAAAT-TACTTAA
* * *
3710 TTGCACCGAACTGAGTTGATTACCAAATTACTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
*
3745 CTACACCGAATTAAGTTGATTACCAAATTACTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
**
3780 TTACACCGAATTAAGTTGATTACCATCTTACTTCTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTA---CTTAA
* * * * *
3818 TTTAATTACCGATTTAATTAATTTAATTTCCAATTTACTTAA
1 -TT-A-CACCG----AATTAAGTTGATTACCAAATTACTTAA
* * *
3860 TTGCACCGAACTGAGTTGATTACCAAATTACTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
3895 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
1 TTACACCGAATTAAGTTGATTACCAAATTACTTAA
3930 TTACACCGAATTAAGTTGATTACCA
1 TTACACCGAATTAAGTTGATTACCA
3955 TCTTACTTCT
Statistics
Matches: 283, Mismatches: 45, Indels: 53
0.74 0.12 0.14
Matches are distributed among these distances:
30 8 0.03
32 3 0.01
33 12 0.04
34 4 0.01
35 166 0.59
36 8 0.03
37 1 0.00
38 17 0.06
39 10 0.04
40 1 0.00
41 11 0.04
42 25 0.09
45 17 0.06
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (35 bp):
TTACACCGAATTAAGTTGATTACCAAATTACTTAA
Found at i:3675 original size:21 final size:20
Alignment explanation
Indices: 3651--3711 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
3641 AATTAAGTTG
3651 ATTACCAAATTACTTAATTTA
1 ATTACC-AATTACTTAATTTA
* *
3672 ATTACCGATTTAATTAATTTA
1 ATTACC-AATTACTTAATTTA
*
3693 ATTTCCAATATACTTAATT
1 ATTACCAAT-TACTTAATT
3712 GCACCGAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTACCAATTACTTAATTTA
Found at i:3840 original size:21 final size:21
Alignment explanation
Indices: 3814--3861 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3804 ATCTTACTTC
*
3814 TTAATTTAATTACCGATTTAA
1 TTAATTTAATTACCAATTTAA
* *
3835 TTAATTTAATTTCCAATTTAC
1 TTAATTTAATTACCAATTTAA
3856 TTAATT
1 TTAATT
3862 GCACCGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATTTAATTACCAATTTAA
Found at i:3849 original size:150 final size:150
Alignment explanation
Indices: 3620--3967 Score: 621
Period size: 150 Copynumber: 2.3 Consensus size: 150
3610 GCTTTAATTT
* * **
3620 CCAATTTACTTAATTGCACCGAATTAAGTTGATTACCAAATTA---CTTAATTTAATTACCGATT
1 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTCTTAATTTAATTACCGATT
3682 TAATTAATTTAATTTCCAATATACTTAATTGCACCGAACTGAGTTGATTACCAAATTACTTAACT
66 TAATTAATTTAATTTCCAATATACTTAATTGCACCGAACTGAGTTGATTACCAAATTACTTAACT
3747 ACACCGAATTAAGTTGATTA
131 ACACCGAATTAAGTTGATTA
3767 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTCTTAATTTAATTACCGATT
1 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTCTTAATTTAATTACCGATT
* *
3832 TAATTAATTTAATTTCCAATTTACTTAATTGCACCGAACTGAGTTGATTACCAAATTACTTAATT
66 TAATTAATTTAATTTCCAATATACTTAATTGCACCGAACTGAGTTGATTACCAAATTACTTAACT
3897 ACACCGAATTAAGTTGATTA
131 ACACCGAATTAAGTTGATTA
3917 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTCTTAA
1 CCAAATTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTCTTAA
3968 ATCTTGACCT
Statistics
Matches: 192, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
147 39 0.20
150 153 0.80
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (150 bp):
CCAAATTACTTAATTACACCGAATTAAGTTGATTACCATCTTACTTCTTAATTTAATTACCGATT
TAATTAATTTAATTTCCAATATACTTAATTGCACCGAACTGAGTTGATTACCAAATTACTTAACT
ACACCGAATTAAGTTGATTA
Found at i:4019 original size:38 final size:38
Alignment explanation
Indices: 3968--4043 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3958 TACTTCTTAA
3968 ATCTTGACCTTGCTCTTTTTTGTTTTGTCTTTGAAGAT
1 ATCTTGACCTTGCTCTTTTTTGTTTTGTCTTTGAAGAT
4006 ATCTTGACCTTGCTCTTTTTTGTTTTGTCTTTGAAGAT
1 ATCTTGACCTTGCTCTTTTTTGTTTTGTCTTTGAAGAT
4044 TTGAAGGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.13, C:0.16, G:0.16, T:0.55
Consensus pattern (38 bp):
ATCTTGACCTTGCTCTTTTTTGTTTTGTCTTTGAAGAT
Found at i:9610 original size:208 final size:205
Alignment explanation
Indices: 9244--9664 Score: 522
Period size: 219 Copynumber: 2.0 Consensus size: 205
9234 TACTCATTAC
* * *
9244 TTTTACGTTAAACATCTTTTTTTTAGATATTACGTTAAACATCTTATTATGATCTAATTGTTAAA
1 TTTTACGTTAAACATCTTTTTTTTAGATATCACCTTAAACATCTTATTATGATCTAATTGTCAAA
* ***
9309 CTTCTTATTATAATAATGATATATTAGTAGTAGTTATATTATCATTACATTTTTTTCTTATCTTT
66 CTTCTTATTATAATAATAATATATTAGTAGTAGTTATATTATCATTACATTACATTCTTATCTTT
* * **
9374 TTTTATCTAATTTTTCTT-CCTCTTTTCTTAGATGATTATGACTATTTCAAAGTTGAGTATTTAA
131 TCTTATCTAATTTTTATTAATTCTTTTCTTAGATGATTATGACTATTTCAAAGTTGAGTATTTAA
9438 TATTTTTTAT
196 TATTTTTTAT
9448 TTTTACGTTAAACATCTTTTTTTTTTTAAGATATCACCTTAAACATCTTATTATGATCTAATTGT
1 TTTTACGTTAAACATC---TTTTTTTT-AGATATCACCTTAAACATCTTATTATGATCTAATTGT
9513 CAAACTTCTTACTATTATAATAATAATATATTAGTAGTAGTAGTAGTTATATTATCATTACATTT
62 CAAACTTC-T--TATTATAATAAT-A-ATA-TA-T--TAGTAGTAGTTATATTATCATTACA--T
* * * * * ** *
9578 TTCTTTCTTATCTTTTTTTATGTAATTTTTCTT-CCTCTTTTCTTGGATGATTATGACTATTTCA
116 TACATTCTTATCTTTTCTTATCTAATTTTTATTAATTCTTTTCTTAGATGATTATGACTATTTCA
9642 AAGTTGAGTATTTAATATTTTTT
181 AAGTTGAGTATTTAATATTTTTT
9665 CCAATAATTT
Statistics
Matches: 195, Mismatches: 7, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
204 16 0.08
207 8 0.04
208 42 0.22
209 1 0.01
211 12 0.06
213 3 0.02
214 2 0.01
215 1 0.01
217 25 0.13
219 85 0.44
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (205 bp):
TTTTACGTTAAACATCTTTTTTTTAGATATCACCTTAAACATCTTATTATGATCTAATTGTCAAA
CTTCTTATTATAATAATAATATATTAGTAGTAGTTATATTATCATTACATTACATTCTTATCTTT
TCTTATCTAATTTTTATTAATTCTTTTCTTAGATGATTATGACTATTTCAAAGTTGAGTATTTAA
TATTTTTTAT
Found at i:10007 original size:47 final size:48
Alignment explanation
Indices: 9920--10015 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 48
9910 AACTATTTTG
* *
9920 ATTCATGAGTGTTATGATTTACTCTAATCTCATAATATTTTTGTATTA
1 ATTCATAAGTGTTATGATTTACTCTAATCTCATAATATTTTGGTATTA
*
9968 ATTCATAAGTGTTATGATTT-GTCTAATCTCATAATATTTTGGTATTA
1 ATTCATAAGTGTTATGATTTACTCTAATCTCATAATATTTTGGTATTA
10015 A
1 A
10016 ACTAACGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 26 0.58
48 19 0.42
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (48 bp):
ATTCATAAGTGTTATGATTTACTCTAATCTCATAATATTTTGGTATTA
Found at i:11173 original size:20 final size:19
Alignment explanation
Indices: 11148--11185 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11138 GAATTTATTA
11148 ATAACCTTATAATTGTTTTG
1 ATAACC-TATAATTGTTTTG
*
11168 ATAACCTCTAATTGTTTT
1 ATAACCTATAATTGTTTT
11186 TTAGTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (19 bp):
ATAACCTATAATTGTTTTG
Found at i:15998 original size:1 final size:1
Alignment explanation
Indices: 15992--16027 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
15982 ATTGGAAGAG
15992 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16028 GCAAGCCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18094 original size:42 final size:42
Alignment explanation
Indices: 18043--18172 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 42
18033 CATCCTCCTC
18043 ATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTAT
1 ATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTAT
* * * * * * * * * *
18085 ATCTTCTTC-A--GTACCATCATCATCTTCATCC--CCCT-C
1 ATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTAT
*
18121 ATCTCCTTCAATTTTGTCTTCACCCTCCTCCTCCTGTCCTAT
1 ATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTAT
*
18163 ATCTTCTTCA
1 ATCTCCTTCA
18173 GTATCATCAC
Statistics
Matches: 60, Mismatches: 22, Indels: 12
0.64 0.23 0.13
Matches are distributed among these distances:
36 8 0.13
37 4 0.07
39 27 0.45
41 4 0.07
42 17 0.28
ACGTcount: A:0.15, C:0.40, G:0.03, T:0.42
Consensus pattern (42 bp):
ATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTAT
Found at i:18121 original size:78 final size:78
Alignment explanation
Indices: 18032--18186 Score: 274
Period size: 78 Copynumber: 2.0 Consensus size: 78
18022 ACCATAATCC
*
18032 TCATCCTCCTCATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTATATCTTCTTCAGT
1 TCATCCCCCTCATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTATATCTTCTTCAGT
*
18097 ACCATCATCATCT
66 ACCATCACCATCT
*
18110 TCATCCCCCTCATCTCCTTCAATTTTGTCTTCACCCTCCTCCTCCTGTCCTATATCTTCTTCAGT
1 TCATCCCCCTCATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTATATCTTCTTCAGT
*
18175 ATCATCACCATC
66 ACCATCACCATC
18187 CACACACTGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.16, C:0.41, G:0.03, T:0.40
Consensus pattern (78 bp):
TCATCCCCCTCATCTCCTTCAATTTTATCTTCACCCTCCTCCTCCTGTCCTATATCTTCTTCAGT
ACCATCACCATCT
Found at i:18579 original size:18 final size:18
Alignment explanation
Indices: 18558--18617 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
18548 ATCTCTGCAA
18558 TCCTCATCCTCTCCTCCT
1 TCCTCATCCTCTCCTCCT
* **
18576 TCCTC-TCCCTTTGTTCCT
1 TCCTCAT-CCTCTCCTCCT
* * *
18594 TCCTCTTGCTCTCCTTCT
1 TCCTCATCCTCTCCTCCT
18612 TCCTCA
1 TCCTCA
18618 CTGATCCCTC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.03, C:0.48, G:0.03, T:0.45
Consensus pattern (18 bp):
TCCTCATCCTCTCCTCCT
Found at i:20661 original size:3 final size:3
Alignment explanation
Indices: 20653--20694 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
20643 AAACTATGAG
20653 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20695 CGAAACAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21682 original size:19 final size:19
Alignment explanation
Indices: 21629--21686 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
21619 ATTTTTATTT
* *
21629 TATTTAAATAAATAAAAAAA
1 TATTAAAATAAA-AAATAAA
*
21649 TATTAAAA-ATTAAAATAAA
1 TATTAAAATA-AAAAATAAA
21668 TATTAAAATAAAAAATAAA
1 TATTAAAATAAAAAATAAA
21687 AAAAAGGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TATTAAAATAAAAAATAAA
Found at i:28828 original size:17 final size:17
Alignment explanation
Indices: 28806--28844 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
28796 AACCAATTGG
28806 AGCATTTTGAAGACCTA
1 AGCATTTTGAAGACCTA
28823 AGCATTTTGAAGACCTA
1 AGCATTTTGAAGACCTA
28840 AGCAT
1 AGCAT
28845 AGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (17 bp):
AGCATTTTGAAGACCTA
Found at i:32595 original size:1 final size:1
Alignment explanation
Indices: 32589--32617 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
32579 ATAGCAGCAG
32589 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32618 AACTTTCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33915 original size:45 final size:45
Alignment explanation
Indices: 33865--33950 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
33855 TATTACTTCT
*
33865 CCAGCTCATCATTAATCCGGGGTAGGGACCTTTTAGTAATTACAC
1 CCAGCTCATCATTAATCCAGGGTAGGGACCTTTTAGTAATTACAC
* * *
33910 CCAGCTTATCATTAATTCAGGGTAGGGATCTTTTAGTAATT
1 CCAGCTCATCATTAATCCAGGGTAGGGACCTTTTAGTAATT
33951 CCACTACTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCAGGGTAGGGACCTTTTAGTAATTACAC
Found at i:40992 original size:14 final size:15
Alignment explanation
Indices: 40975--41007 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40965 TTATTTTGTC
*
40975 TAAAAAA-GAAGGGT
1 TAAAAAATGAAAGGT
40989 TAAAAAATGAAAGGT
1 TAAAAAATGAAAGGT
41004 TAAA
1 TAAA
41008 TTTCTATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (15 bp):
TAAAAAATGAAAGGT
Found at i:54652 original size:33 final size:31
Alignment explanation
Indices: 54545--54656 Score: 127
Period size: 33 Copynumber: 3.5 Consensus size: 31
54535 CTCGTCACCT
* *
54545 AAAACAGATTTATTTTCAATGCTA-TCAACC
1 AAAACAGAATTATTTTTAATGCTATTCAACC
* *
54575 AAAACAGGATTATTTGTAATGCTATAATCAACC
1 AAAACAGAATTATTTTTAATGCTAT--TCAACC
*
54608 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTTAATGCTA--TTCAACC
*
54641 AAAACAGAATTGTTTT
1 AAAACAGAATTATTTT
54657 CATCACAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
30 20 0.29
33 49 0.70
35 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (31 bp):
AAAACAGAATTATTTTTAATGCTATTCAACC
Found at i:56255 original size:8 final size:8
Alignment explanation
Indices: 56227--56260 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
56217 GAATCGGCTA
56227 TGAATTTT
1 TGAATTTT
*
56235 TGAAGTTTC
1 TGAA-TTTT
56244 TGAATTTT
1 TGAATTTT
56252 TGAATTTT
1 TGAATTTT
56260 T
1 T
56261 CAATAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:57260 original size:33 final size:34
Alignment explanation
Indices: 57215--57296 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 34
57205 GGTTGGTGCG
*
57215 CCAAG-CG-ATGGCCGGTTG-TGGCCGGACATGT
1 CCAAGTCGCATGGCCGGTTGATGGCCGGACATCT
* * * *
57246 CCATGTCGCGTGGCCGG-TGATGGCCGGGCTTCT
1 CCAAGTCGCATGGCCGGTTGATGGCCGGACATCT
57279 CCAAGTCGCATGGCCGGT
1 CCAAGTCGCATGGCCGGT
57297 CACTCGCGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
31 4 0.10
32 4 0.10
33 32 0.80
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (34 bp):
CCAAGTCGCATGGCCGGTTGATGGCCGGACATCT
Found at i:59276 original size:27 final size:27
Alignment explanation
Indices: 59200--59277 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
59190 AAGTGGACTA
*
59200 AAAAATGACCAAAATGCCCCCAGGATGT
1 AAAAATGACCAAAATG-CCCCTGGATGT
59228 -AAAATGACCAAAATGCCCCTGGATGT
1 AAAAATGACCAAAATGCCCCTGGATGT
*
59254 AAAAATGACCAAAATGCCTCTGGA
1 AAAAATGACCAAAATGCCCCTGGA
59278 CGACCCTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 10 0.21
27 37 0.79
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGATGT
Found at i:63030 original size:33 final size:33
Alignment explanation
Indices: 62990--63082 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
62980 AGCACTTGTG
* *
62990 ACCGGCCACGCGACTTGGAGATGCCC-AGCCATC
1 ACCGGCCACGCGACATGGACATGCCCGA-CCATC
63023 ACCGGCCACGCGACATGGACATGCCCGACCATC
1 ACCGGCCACGCGACATGGACATGCCCGACCATC
* *
63056 ACCGACCACGCGACATGGTCATGCCCG
1 ACCGGCCACGCGACATGGACATGCCCG
63083 GCCACATGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.23, C:0.41, G:0.26, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGCCCGACCATC
Found at i:64114 original size:9 final size:9
Alignment explanation
Indices: 64102--64126 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
64092 GAAAAATATC
64102 AAAAAAATT
1 AAAAAAATT
64111 AAAAAAATT
1 AAAAAAATT
64120 AAAAAAA
1 AAAAAAA
64127 CTTTCGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:69491 original size:33 final size:33
Alignment explanation
Indices: 69451--69555 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 33
69441 AGCACTTGTG
* *
69451 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGACATGCCCGGCCATC
69484 ACCGGCCACGCGACATGGACATGCCCGGCCATC
1 ACCGGCCACGCGACATGGACATGCCCGGCCATC
* **
69517 ACCGACCACGCGACATGGACATAACCGGCCA-C
1 ACCGGCCACGCGACATGGACATGCCCGGCCATC
69549 AACCGGC
1 -ACCGGC
69556 TACATGATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 1 0.02
33 64 0.98
ACGTcount: A:0.24, C:0.41, G:0.27, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGCCCGGCCATC
Found at i:70538 original size:15 final size:15
Alignment explanation
Indices: 70515--70547 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
70505 CACATCATAT
70515 ATTCCATTAATTTGC
1 ATTCCATTAATTTGC
*
70530 ATTCTATTAATTTGC
1 ATTCCATTAATTTGC
70545 ATT
1 ATT
70548 AGTGGTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTCCATTAATTTGC
Found at i:73792 original size:18 final size:20
Alignment explanation
Indices: 73751--73791 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
73741 GAGAGGGAAG
73751 AAAGAAGAAGGAAAAACAAA
1 AAAGAAGAAGGAAAAACAAA
* *
73771 AAAG-AGAAGAAAAAATAAA
1 AAAGAAGAAGGAAAAACAAA
73790 AA
1 AA
73792 GGAATCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAGAAGAAGGAAAAACAAA
Found at i:76657 original size:8 final size:8
Alignment explanation
Indices: 76644--76668 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
76634 ATCTTCAATG
76644 GTCTTCAA
1 GTCTTCAA
76652 GTCTTCAA
1 GTCTTCAA
76660 GTCTTCAA
1 GTCTTCAA
76668 G
1 G
76669 ATGAGTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (8 bp):
GTCTTCAA
Found at i:86645 original size:21 final size:20
Alignment explanation
Indices: 86606--86647 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
86596 TCCTTTGCTT
*
86606 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
86626 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
86647 A
1 A
86648 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:86974 original size:16 final size:15
Alignment explanation
Indices: 86950--86979 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
86940 TATAAATTTC
86950 AAAAATGTGTTTTAA
1 AAAAATGTGTTTTAA
86965 AAAAATTGTGTTTTA
1 AAAAA-TGTGTTTTA
86980 TATCTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
AAAAATGTGTTTTAA
Found at i:91552 original size:81 final size:78
Alignment explanation
Indices: 91421--91568 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 78
91411 GTGCTTAACC
* *
91421 TGATATACAACCTAACATAAAAGGACAAAATGATACTGAGATGCAATATATTCGTTTTTT-TAAA
1 TGATATACAACCTAACATAAAAGGACAAAATGAAAATGAGATGCAATATATTCGTTTTTTCTAAA
91485 GCATTTTTTTAGG
66 GCATTTTTTTAGG
*
91498 TGATATACAACCTAACATATATAAAAGGATAAAATGAAAATGAGATGCAATATATTCGTTTTTTC
1 TGATATACAACCTAAC----ATAAAAGGACAAAATGAAAATGAGATGCAATATATTCGTTTTTTC
91563 TAAAGC
62 TAAAGC
91569 TAGGTGTTCA
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
77 16 0.25
81 41 0.65
82 6 0.10
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (78 bp):
TGATATACAACCTAACATAAAAGGACAAAATGAAAATGAGATGCAATATATTCGTTTTTTCTAAA
GCATTTTTTTAGG
Found at i:93927 original size:13 final size:13
Alignment explanation
Indices: 93909--93933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93899 ATATCTCATA
93909 CCAGGATAAACTG
1 CCAGGATAAACTG
93922 CCAGGATAAACT
1 CCAGGATAAACT
93934 AAAATACACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (13 bp):
CCAGGATAAACTG
Found at i:93948 original size:23 final size:23
Alignment explanation
Indices: 93918--93961 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
93908 ACCAGGATAA
93918 ACTGCCAGGATAAACTAAAATAC
1 ACTGCCAGGATAAACTAAAATAC
93941 ACTGCCAGGATAAACTAAAAT
1 ACTGCCAGGATAAACTAAAAT
93962 TGCAATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (23 bp):
ACTGCCAGGATAAACTAAAATAC
Found at i:95425 original size:21 final size:21
Alignment explanation
Indices: 95401--95489 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 21
95391 TTGAAAGAAG
*
95401 AAACTTGGTTAAAAAACTTGA
1 AAACTTGGTTAAAAACCTTGA
* *
95422 AAACTTGGACTTTGTTAAAAACCTCGG
1 AAACTT-G-----GTTAAAAACCTTGA
95449 AAACTTGGTTAAAAACCTTGA
1 AAACTTGGTTAAAAACCTTGA
95470 AAACTT-GTTAAAAACCTTGA
1 AAACTTGGTTAAAAACCTTGA
95490 TCGATCTCCC
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
20 14 0.25
21 24 0.42
22 1 0.02
26 1 0.02
27 17 0.30
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (21 bp):
AAACTTGGTTAAAAACCTTGA
Found at i:95433 original size:27 final size:27
Alignment explanation
Indices: 95403--95456 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
95393 GAAAGAAGAA
*
95403 ACTTGGTTAAAAAACTTGAAAACTTGG
1 ACTTGGTTAAAAAACTCGAAAACTTGG
* * *
95430 ACTTTGTTAAAAACCTCGGAAACTTGG
1 ACTTGGTTAAAAAACTCGAAAACTTGG
95457 TTAAAAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (27 bp):
ACTTGGTTAAAAAACTCGAAAACTTGG
Found at i:100791 original size:3 final size:3
Alignment explanation
Indices: 100783--100808 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
100773 AAAAAATTTA
100783 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
100809 AGAAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:101197 original size:10 final size:10
Alignment explanation
Indices: 101182--101211 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
101172 TCCAAGCCTA
101182 TTGATTATTC
1 TTGATTATTC
101192 TTGATTATTC
1 TTGATTATTC
101202 TTGATTATTC
1 TTGATTATTC
101212 CATCAATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (10 bp):
TTGATTATTC
Found at i:104625 original size:2 final size:2
Alignment explanation
Indices: 104618--104651 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
104608 TACTAACTTG
104618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104652 TTAACACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107326 original size:5 final size:5
Alignment explanation
Indices: 107312--107342 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
107302 AATGGTATAA
107312 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
107343 CATGGGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:108464 original size:12 final size:13
Alignment explanation
Indices: 108444--108475 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
108434 CTGCAAAATT
108444 AACAAAAACAAAA
1 AACAAAAACAAAA
108457 AA-AAAAACAAAA
1 AACAAAAACAAAA
108469 AACAAAA
1 AACAAAA
108476 TACGAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AACAAAAACAAAA
Found at i:115265 original size:27 final size:27
Alignment explanation
Indices: 115191--115266 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
115181 TAGGGTCACC
*
115191 CAGGGGCATTTTGGTCATTTGTGCACT
1 CAGGGGCATTTTGGTCATTTTTGCACT
115218 CAGGGGCATTTTGGTCATTTTTGCACT
1 CAGGGGCATTTTGGTCATTTTTGCACT
*
115245 CAGGGGCATTTTAGTCATTTTT
1 CAGGGGCATTTTGGTCATTTTT
115267 AAGTTCACCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTTTGCACT
Found at i:119200 original size:55 final size:55
Alignment explanation
Indices: 119135--119529 Score: 673
Period size: 55 Copynumber: 7.2 Consensus size: 55
119125 TAAAAGGGGT
* * * *
119135 AATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTCAAAGTGATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
119190 AATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
119245 AATCAATAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
119300 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
119355 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGTAATAGTAATTAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
119410 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGACAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
*
119465 AATCAGTAATTAAGTAAAAAGAGATTAATCAAAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
119520 AATCAGTAAT
1 AATCAGTAAT
119530 CAGGGAAAAG
Statistics
Matches: 327, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 327 1.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:119414 original size:29 final size:29
Alignment explanation
Indices: 119381--119470 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
119371 AAAAGAGATT
*
119381 AATCAGAGACAAGGTAATAGTAATTAGTA
1 AATCAGAGACAAGGTAATAGTAATCAGTA
* * *
119410 AATCAGTA-ATTAA-GTAA-A--AA-GAGATT
1 AATCAG-AGA-CAAGGTAATAGTAATCAG-TA
119436 AATCAGAGACAAGGTAATAGTAATCAGTA
1 AATCAGAGACAAGGTAATAGTAATCAGTA
119465 AATCAG
1 AATCAG
119471 TAATTAAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 18
0.66 0.09 0.26
Matches are distributed among these distances:
25 5 0.11
26 14 0.30
27 1 0.02
28 1 0.02
29 20 0.43
30 5 0.11
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (29 bp):
AATCAGAGACAAGGTAATAGTAATCAGTA
Found at i:119858 original size:64 final size:64
Alignment explanation
Indices: 119784--120085 Score: 237
Period size: 64 Copynumber: 4.7 Consensus size: 64
119774 AATAGCATGC
* * * * * * *
119784 AATCAGTAAAAAGTAAAAAGGT-ATCTGA-AAGGGTAAAATGGTAATTAGTAAAGAGTAAAATAG
1 AATCAGTAAAAAGTAAAAAGATAATC-AACAAGAGTAAAATAGTAATCAGTAAAAAGT-AAACAG
119847 T
64 T
* *
119848 AATCAGTAAAAAGTAAGAAGATAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAACAGT
1 AATCAGTAAAAAGTAAAAAGATAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAACAGT
* * * * * *
119912 AATCAGT-AAGAGTAAAATAG-TAAT-AAGTAAGAAGTAAAA-GGAAATCAGT-AAGAGTAAAAA
1 AATCAGTAAAAAGTAAAA-AGATAATCAA-CAAG-AGTAAAATAGTAATCAGTAAAAAGTAAACA
119972 GGT
63 -GT
* * * * * *
119975 GATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAA-AGGTAATCATTAAAAAGCAAA-AG
1 AATCAGTAAAAAGTAAAAAGATAATCAACAAG-AGTAAAATA-GTAATCAGTAAAAAGTAAACA-
*
120038 GC
63 GT
*
120040 AATCAGCAAAAAGT-AAAAGAGTAATCAACAAGAGTAAAATAGTAAT
1 AATCAGTAAAAAGTAAAAAGA-TAATCAACAAGAGTAAAATAGTAAT
120086 TAGTGCAACA
Statistics
Matches: 194, Mismatches: 31, Indels: 26
0.77 0.12 0.10
Matches are distributed among these distances:
62 11 0.06
63 32 0.16
64 85 0.44
65 59 0.30
66 7 0.04
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.19
Consensus pattern (64 bp):
AATCAGTAAAAAGTAAAAAGATAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAACAGT
Found at i:119883 original size:43 final size:42
Alignment explanation
Indices: 119834--120066 Score: 231
Period size: 43 Copynumber: 5.5 Consensus size: 42
119824 GTAATTAGTA
*
119834 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGATAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGATAATCAGC
* *
119877 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAACAG-TAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGATAATCAGC
* * *
119919 AAGAGTAAAATAGTAATAAGTAAGAAGTAAAAGGA-AATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAA-GATAATCAGC
* * *
119961 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGATAATCAGC
* * **
120004 AAGAAGTAAAA-AGGTAATCATTAAAAAGCAAAAGGCAATCAGC
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGATAATCAGC
* *
120047 AAAAAGTAAAAGAGTAATCA
1 -AAGAGTAAAATAGTAATCA
120067 ACAAGAGTAA
Statistics
Matches: 162, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
41 2 0.01
42 66 0.41
43 70 0.43
44 24 0.15
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGATAATCAGC
Found at i:119917 original size:21 final size:20
Alignment explanation
Indices: 119784--120058 Score: 130
Period size: 21 Copynumber: 12.9 Consensus size: 20
119774 AATAGCATGC
119784 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAA-GT
* **
119806 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAAAGTAAAA--GT
* *
119826 AATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGT-AAA-AGT
119848 AATCAGTAAAAAGTAAGAAGAT
1 AATCAGTAAAAAGTAA-AAG-T
*
119870 AATCA--ACAAGAGTAAAATAGT
1 AATCAGTA-AAAAGT-AAA-AGT
*
119891 AGTCAGTAAAAAGTAAACAGT
1 AATCAGTAAAAAGTAAA-AGT
*
119912 AATCAGT-AAGAGTAAAATAGT
1 AATCAGTAAAAAGT-AAA-AGT
* * *
119933 AATAAGTAAGAAGTAAAAGGA
1 AATCAGTAAAAAGTAAAA-GT
*
119954 AATCAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAA-GT
* *
119975 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAAAGT-AAAAG-T
* *
119997 AATCAGCAAGAAGTAAAAAGGT
1 AATCAGTAAAAAGT-AAAA-GT
* * *
120019 AATCATTAAAAAGCAAAAGGC
1 AATCAGTAAAAAGTAAAA-GT
*
120040 AATCAGCAAAAAGTAAAAG
1 AATCAGTAAAAAGTAAAAG
120059 AGTAATCAAC
Statistics
Matches: 198, Mismatches: 36, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
19 4 0.02
20 20 0.10
21 90 0.45
22 78 0.39
23 5 0.03
24 1 0.01
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCAGTAAAAAGTAAAAGT
Found at i:120036 original size:22 final size:22
Alignment explanation
Indices: 119784--120066 Score: 149
Period size: 22 Copynumber: 13.2 Consensus size: 22
119774 AATAGCATGC
*
119784 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGCAAAAAGTAAAAAGGT
* ** *
119806 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGCAAAAAGTAAAAAGGT
* * *
119826 AATTAGTAAAGAGTAAAATA-GT
1 AATCAGCAAAAAGTAAAA-AGGT
* * *
119848 AATCAGTAAAAAGTAAGAAGAT
1 AATCAGCAAAAAGTAAAAAGGT
* *
119870 AATCAAC-AAGAGTAAAATA-GT
1 AATCAGCAAAAAGTAAAA-AGGT
* * *
119891 AGTCAGTAAAAAGTAAACA-GT
1 AATCAGCAAAAAGTAAAAAGGT
* *
119912 AATCAG-TAAGAGTAAAATA-GT
1 AATCAGCAAAAAGTAAAA-AGGT
* * * *
119933 AATAAGTAAGAAGT-AAAAGGA
1 AATCAGCAAAAAGTAAAAAGGT
* *
119954 AATCAG-TAAGAGTAAAAAGGT
1 AATCAGCAAAAAGTAAAAAGGT
* * * *
119975 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGCAAAAAGTAAAAAGGT
*
119997 AATCAGCAAGAAGTAAAAAGGT
1 AATCAGCAAAAAGTAAAAAGGT
** * *
120019 AATCATTAAAAAG-CAAAAGGC
1 AATCAGCAAAAAGTAAAAAGGT
120040 AATCAGCAAAAAGT-AAAAGAGT
1 AATCAGCAAAAAGTAAAAAG-GT
120062 AATCA
1 AATCA
120067 ACAAGAGTAA
Statistics
Matches: 196, Mismatches: 52, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
20 25 0.13
21 79 0.40
22 92 0.47
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.19
Consensus pattern (22 bp):
AATCAGCAAAAAGTAAAAAGGT
Found at i:120075 original size:21 final size:20
Alignment explanation
Indices: 119833--120085 Score: 90
Period size: 21 Copynumber: 11.9 Consensus size: 20
119823 GGTAATTAGT
*
119833 AAAGAGTAAAATAGTAATCA
1 AAAGAGTAAAAGAGTAATCA
*
119853 GTAAAAAGTAAGAAGA-TAATCA
1 --AAAGAGTAA-AAGAGTAATCA
* *
119875 ACAAGAGTAAAATAGTAGTCA
1 A-AAGAGTAAAAGAGTAATCA
* *
119896 GTAAAAAGT-AAACAGTAATCA
1 --AAAGAGTAAAAGAGTAATCA
* *
119917 GTAAGAGTAAAATAGTAAT-A
1 -AAAGAGTAAAAGAGTAATCA
*
119937 AGTAAGAAGTAAAAG-GAAATCA
1 A--AAG-AGTAAAAGAGTAATCA
* *
119959 GTAAGAGTAAAA-AGGTGATCA
1 -AAAGAGTAAAAGA-GTAATCA
119980 GTAAAGAGTAAAA-AGCTAATCA
1 --AAAGAGTAAAAGAG-TAATCA
*
120002 GCAAGAAGTAAAA-AGGTAATCA
1 -AAAG-AGTAAAAGA-GTAATCA
* * *
120024 TTAAAAAGCAAAAG-GCAATCA
1 --AAAGAGTAAAAGAGTAATCA
*
120045 GCAAAAAGTAAAAGAGTAATCA
1 --AAAGAGTAAAAGAGTAATCA
*
120067 ACAAGAGTAAAATAGTAAT
1 A-AAGAGTAAAAGAGTAAT
120086 TAGTGCAACA
Statistics
Matches: 176, Mismatches: 34, Indels: 43
0.70 0.13 0.17
Matches are distributed among these distances:
20 18 0.10
21 82 0.47
22 69 0.39
23 7 0.04
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (20 bp):
AAAGAGTAAAAGAGTAATCA
Found at i:121067 original size:36 final size:36
Alignment explanation
Indices: 121027--121096 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
121017 ATTTTCTCTA
*
121027 ATTTATTTCATCAATGTCTAAAGACATTGACTAATC
1 ATTTATTTCATCAATGTCTAAAGACATCGACTAATC
*
121063 ATTTATTTCATCAATGTCTCAAGACATCGACTAA
1 ATTTATTTCATCAATGTCTAAAGACATCGACTAA
121097 ATCTCCATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.37
Consensus pattern (36 bp):
ATTTATTTCATCAATGTCTAAAGACATCGACTAATC
Done.